NM_138962.4:c.405+16263C>A

Variant names:

• chr17-57417734-C-A
• rs9892791
• NM_138962.4:c.405+16263C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138962.4(MSI2):​c.405+16263C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,006 control chromosomes in the GnomAD database, including 36,610 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.69 (36610 hom., cov: 31)
• Consequence: MSI2 NM_138962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 2 publications found

Genes affected

MSI2 (HGNC:18585): (musashi RNA binding protein 2) This gene encodes an RNA-binding protein that is a member of the Musashi protein family. The encoded protein is transcriptional regulator that targets genes involved in development and cell cycle regulation. Mutations in this gene are associated with poor prognosis in certain types of cancers. This gene has also been shown to be rearranged in certain cancer cells. [provided by RefSeq, Apr 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138962.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	NM_138962.4	MANE Select	c.405+16263C>A		intron	N/A	NP_620412.1
	MSI2	NM_001322250.2		c.339+16263C>A		intron	N/A	NP_001309179.1
	MSI2	NM_001322251.2		c.405+16263C>A		intron	N/A	NP_001309180.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSI2	ENST00000284073.7	TSL:1 MANE Select	c.405+16263C>A		intron	N/A	ENSP00000284073.2
	MSI2	ENST00000579180.2	TSL:1	c.93+16263C>A		intron	N/A	ENSP00000462264.1
	MSI2	ENST00000675656.1		c.366+16263C>A		intron	N/A	ENSP00000501595.1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105037 AN: 151888 Hom.: 36582 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.709

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.692 AC: 105120 AN: 152006 Hom.: 36610 Cov.: 31 AF XY: 0.696 AC XY: 51699 AN XY: 74288

African (AFR) AF: 0.653 AC: 27082 AN: 41448

American (AMR) AF: 0.743 AC: 11354 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2763 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4786 AN: 5156

South Asian (SAS) AF: 0.790 AC: 3806 AN: 4818

European-Finnish (FIN) AF: 0.652 AC: 6897 AN: 10572

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46064 AN: 67952

Other (OTH) AF: 0.712 AC: 1505 AN: 2114

Alfa AF: 0.691 Hom.: 68583

Bravo AF: 0.701

Asia WGS AF: 0.837 AC: 2911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9892791; hg19: chr17-55495095;